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I came from India on F1 visa in 2008 for my MS. I finished my MS degree in 2011. I paid around 15000 USD in 2010 for my college fee. I went to one of the tax office and I got wrong advise.I filed tuition credit return in 2011 and got around 1500 USD back.

I was not told that MS student could not file that tuition credit. Only undergraduate students were eligible for that. I filed saying that I am 3rd year college student, because I came in USA in 2008 and I was running 3rd year during 2010.

Currently I am on H1b and company is filing green card. Will I be in trouble during background process or should I file tax amendment?

Adjustment of status to lawful permanent resident is at the discretion of the Attorney General. Although good moral character is not statutorily required for adjustment of status it can be considered as a factor at the discretion of the Attorney General.

I agree with the comment above that you should hire a CPA and get your prior tax return correctly amended so that your earlier mistake is not construed as a willful misrepresentation which could be considered an adverse factor when you are adjusting status.